Contacts of the helix formed by residues 160 - 178 (chain B) in PDB entry 4A9N
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASP 160 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156B ASN* 3.5 12.8 - - + +
157B LYS* 2.9 53.6 + - - +
158B PRO 4.2 0.5 - - - +
159B THR* 1.3 80.9 + - - +
161B ASP* 1.3 65.6 + - - +
162B ILE* 4.0 17.3 - - + -
163B VAL* 3.1 18.8 + - + +
164B LEU* 3.7 3.5 + - - +
1189B A9N 5.9 0.4 - - - +
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Residues in contact with ASP 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159B THR 4.3 4.9 - - - +
160B ASP* 1.3 71.5 - - - +
162B ILE* 1.3 63.3 + - - +
164B LEU* 3.0 23.3 + - + +
165B MET* 3.0 21.4 + - + +
1189B A9N 4.2 15.7 - - + -
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Residues in contact with ILE 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B PRO* 3.5 39.0 - - + -
99B PHE* 3.6 17.5 - - + -
152B CYS* 3.6 15.5 - - - -
156B ASN* 3.4 39.3 - - + +
160B ASP* 4.0 8.5 - - + +
161B ASP* 1.3 77.9 - - - +
163B VAL* 1.3 59.7 + - - +
165B MET* 3.2 8.3 + - - +
166B ALA* 2.8 28.1 + - - +
1189B A9N 3.9 44.6 + - + +
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Residues in contact with VAL 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A ILE* 3.8 29.6 - - + -
152B CYS* 4.4 12.1 - - - +
153B TYR* 3.8 12.9 - - + +
156B ASN* 3.9 20.2 - - + +
157B LYS 3.4 25.8 - - - +
158B PRO* 3.8 15.7 - - + +
160B ASP 3.1 10.0 + - - +
162B ILE* 1.3 78.3 - - + +
164B LEU* 1.3 58.7 + - - +
166B ALA* 3.3 4.0 + - - +
167B GLN* 2.9 35.5 + - - +
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Residues in contact with LEU 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B PHE* 5.3 6.1 - - + -
160B ASP 3.7 3.0 + - - +
161B ASP* 3.0 16.7 + - - +
163B VAL* 1.3 80.1 - - - +
165B MET* 1.3 61.9 + - + +
167B GLN* 3.3 20.5 + - + +
168B THR* 3.0 35.7 + - - +
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Residues in contact with MET 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B PHE* 3.6 57.8 - - + +
97B TRP* 3.8 16.6 - - - +
98B PRO* 3.7 20.4 - - + -
99B PHE* 4.4 4.0 - - + -
161B ASP* 3.0 21.1 + - + +
162B ILE* 3.5 9.9 - - - +
164B LEU* 1.3 74.8 - - + +
166B ALA* 1.3 64.6 + - - +
168B THR* 3.3 3.1 + - - -
169B LEU* 3.1 29.7 + - - +
1187B EDO 3.8 10.3 - - - +
1189B A9N 3.8 28.3 - - + -
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Residues in contact with ALA 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B PHE* 3.8 14.4 - - + -
149B PHE* 3.7 15.8 - - + -
152B CYS* 3.8 18.6 - - + -
153B TYR* 3.4 21.3 - - + +
162B ILE 2.8 20.9 + - - +
163B VAL 3.6 4.5 - - - +
165B MET* 1.3 72.6 - - - +
167B GLN* 1.3 52.0 - - - +
169B LEU* 3.2 1.7 + - - -
170B GLU* 2.8 36.9 + - - +
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Residues in contact with GLN 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A ASN* 5.5 0.2 + - - -
150A THR* 4.2 8.8 - - + +
154A ILE* 3.7 23.5 - - - +
1188A EDO 4.0 26.2 - - - -
153B TYR* 3.3 22.4 + - + +
163B VAL* 2.9 24.2 + - - +
164B LEU* 3.5 28.0 - - + +
166B ALA* 1.3 75.7 - - - +
168B THR* 1.3 62.2 - - - +
170B GLU* 3.7 3.1 - - - +
171B LYS* 3.0 40.9 + - + +
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Residues in contact with THR 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B HIS* 4.0 18.8 - - + +
95B PHE* 3.8 28.8 - - + -
164B LEU* 3.0 20.9 + - - +
165B MET 3.6 7.6 - - - -
167B GLN* 1.3 76.1 - - - +
169B LEU* 1.3 62.3 + - - +
171B LYS* 3.3 12.4 + - - +
172B ILE* 3.2 26.9 + - + +
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Residues in contact with LEU 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90B LEU* 3.2 32.4 - - + +
93B HIS* 3.6 42.0 - - + +
95B PHE* 3.5 24.9 - - + +
96B ALA* 3.9 7.6 - - + +
99B PHE* 3.5 30.3 - - + -
123B MET* 5.8 4.3 - - + -
148B MET* 6.3 0.4 - - + -
149B PHE* 3.8 15.3 - - + -
165B MET 3.1 17.7 + - - +
166B ALA 3.7 3.1 - - - +
168B THR* 1.3 74.9 - - - +
170B GLU* 1.3 58.3 + - - +
172B ILE* 3.2 3.4 + - - -
173B PHE* 2.9 25.3 + - - +
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Residues in contact with GLU 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A ASN* 3.1 32.7 + - - +
150A THR* 2.9 18.2 + - - +
153A TYR* 6.0 1.0 - - - -
170A GLU* 4.9 1.4 - - - +
146B ASN* 4.7 9.2 - - - +
149B PHE* 3.4 40.8 - - + +
150B THR* 5.2 1.2 + - - -
153B TYR* 2.5 30.0 + - - +
166B ALA 2.8 21.5 + - - +
167B GLN* 3.7 5.1 - - - +
169B LEU* 1.3 73.2 - - - +
171B LYS* 1.3 61.5 + - - +
173B PHE* 3.3 6.3 + - + +
174B LEU* 3.0 26.4 + - + +
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Residues in contact with LYS 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A GLN* 5.2 6.2 + - - +
143A GLN* 2.9 45.7 + - - +
146A ASN* 4.9 9.2 - - - +
147A THR* 4.1 13.9 + - - -
1189A EDO 3.9 32.4 + - - -
167B GLN* 3.0 33.2 + - + +
168B THR* 3.6 8.7 - - - +
170B GLU* 1.3 76.0 - - - +
172B ILE* 1.3 61.0 + - + +
174B LEU* 3.4 1.3 + - - -
175B GLN* 3.0 16.7 + - - +
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Residues in contact with ILE 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B ALA* 4.9 7.6 - - + +
90B LEU* 3.8 15.3 - - + +
93B HIS* 3.4 39.5 - - + +
168B THR* 3.2 18.9 + - + +
169B LEU* 3.2 11.0 + - - +
171B LYS* 1.3 72.7 - - + +
173B PHE* 1.3 67.9 + - - +
175B GLN* 3.2 15.8 + - - +
176B LYS* 3.0 46.9 + - + +
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Residues in contact with PHE 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174A LEU* 4.6 13.0 - - + -
82B LEU* 4.7 1.8 - - + -
86B VAL* 3.6 21.5 - - + -
90B LEU* 3.9 13.2 - - + +
142B MET* 3.9 23.1 - - + -
145B PHE* 3.4 50.0 - + + -
146B ASN* 5.5 2.2 - - + -
149B PHE* 4.3 12.1 - + + -
169B LEU 2.9 14.0 + - - +
170B GLU* 3.3 16.8 - - + +
172B ILE* 1.3 77.4 - - - +
174B LEU* 1.3 74.4 + - + +
176B LYS* 3.4 2.0 + - - +
177B VAL* 2.9 55.5 + - + +
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Residues in contact with LEU 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139A SER* 5.7 1.1 - - - +
142A MET* 3.5 40.4 - - + +
143A GLN* 3.9 17.5 - - - +
146A ASN* 3.2 45.1 - - + +
173A PHE* 4.3 18.4 - - + -
174A LEU* 4.9 7.2 - - + -
177A VAL* 5.6 0.9 - - + -
170B GLU* 3.0 17.4 + - + +
171B LYS 3.8 4.0 - - - +
172B ILE 3.2 0.2 - - - -
173B PHE* 1.3 90.6 - - + +
175B GLN* 1.3 65.7 + - - +
177B VAL* 3.3 5.5 + - + -
178B ALA* 3.0 20.1 + - - +
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Residues in contact with GLN 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139A SER* 4.6 16.8 + - - +
143A GLN* 3.8 14.0 - - - +
1189A EDO 6.0 3.8 - - - -
171B LYS* 3.0 17.2 + - - +
172B ILE* 3.5 20.9 - - - +
174B LEU* 1.3 77.8 - - - +
176B LYS* 1.3 69.0 + - + +
178B ALA* 3.4 18.6 - - - +
179B SER* 4.0 6.4 + - - -
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Residues in contact with LYS 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81B TYR* 2.7 30.3 + - - +
85B VAL* 4.5 14.7 + - + +
86B VAL* 3.9 22.7 - - + +
89B ALA* 3.0 38.4 - - + +
90B LEU* 6.4 0.2 - - + -
172B ILE* 3.0 33.2 + - + +
173B PHE 3.8 3.4 - - - +
175B GLN* 1.3 78.7 - - + +
177B VAL* 1.3 65.4 + - - +
179B SER* 3.1 8.2 + - - -
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Residues in contact with VAL 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A MET* 4.5 2.7 - - + -
177A VAL* 3.8 19.6 - - + +
180A MET* 4.9 2.4 - - - +
81B TYR* 4.7 1.3 - - - -
82B LEU* 4.2 17.3 - - + -
86B VAL* 4.6 2.7 - - + -
142B MET* 3.8 27.4 - - + -
173B PHE* 2.9 54.5 + - + +
174B LEU* 3.8 9.6 - - + +
176B LYS* 1.3 75.5 - - - +
178B ALA* 1.3 63.5 + - - +
180B MET* 3.0 28.7 + - + +
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Residues in contact with ALA 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A GLN* 3.0 30.5 + - - +
139A SER* 4.5 15.7 - - - +
142A MET* 4.0 17.9 - - - -
180A MET* 3.7 16.9 - - + +
181A PRO 4.1 1.9 - - - +
182A GLN* 3.6 2.3 - - - +
174B LEU 3.0 13.3 + - - +
175B GLN 3.4 13.9 - - - +
176B LYS 3.2 0.6 - - - -
177B VAL* 1.3 76.5 - - - +
179B SER* 1.3 59.3 + - - +
180B MET 3.4 1.5 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il